Data_Sheet_1_Mendelian randomization analysis suggests no associations of human herpes viruses with amyotrophic lateral sclerosis.doc

BackgroundThe causal associations between infections with human herpes viruses (HHVs) and amyotrophic lateral sclerosis (ALS) has been disputed. This study investigated the causal associations between herpes simplex virus (HSV), varicella-zoster virus (VZV), Epstein–Barr virus (EBV), cytomegalovirus (CMV), HHV-6, and HHV-7 infections and ALS through a bidirectional Mendelian randomization (MR) method.MethodsThe genome-wide association studies (GWAS) database were analyzed by inverse variance weighted (IVW), MR-Egger, weighted median, simple mode, and weighted mode methods. MR-Egger intercept test, MR-PRESSO test, Cochran’s Q test, funnel plots, and leaveone-out analysis were used to verify the validity and robustness of the MR results.ResultsIn the forward MR analysis of the IVW, genetically predicted HSV infections [odds ratio (OR) = 0.9917; 95% confidence interval (CI): 0.9685–1.0154; p = 0.4886], HSV keratitis and keratoconjunctivitis (OR = 0.9897; 95% CI: 0.9739–1.0059; p = 0.2107), anogenital HSV infection (OR = 1.0062; 95% CI: 0.9826–1.0304; p = 0.6081), VZV IgG (OR = 1.0003; 95% CI: 0.9849–1.0160; p = 0.9659), EBV IgG (OR = 0.9509; 95% CI: 0.8879–1.0183; p = 0.1497), CMV (OR = 0.9481; 95% CI: 0.8680–1.0357; p = 0.2374), HHV-6 IgG (OR = 0.9884; 95% CI: 0.9486–1.0298; p = 0.5765) and HHV-7 IgG (OR = 0.9991; 95% CI: 0.9693–1.0299; p = 0.9557) were not causally associated with ALS. The reverse MR analysis of the IVW revealed comparable findings, indicating no link between HHVs infections and ALS. The reliability and validity of the findings were verified by the sensitivity analysis.ConclusionAccording to the MR study, there is no evidence of causal associations between genetically predicted HHVs (HSV, VZV, EBV, CMV, HHV-6, and HHV-7) and ALS.</p

Combining the Masking and Scaffolding Modalities of Colloidal Crystal Templates: Plasmonic Nanoparticle Arrays with Multiple Periodicities

Surface patterns with prescribed structures and properties are highly desirable for a variety of applications. Increasing the heterogeneity of surface patterns is frequently required. This work opens a new avenue toward creating nanoparticle arrays with multiple periodicities by combining two generally separately applied modalities (i.e., scaffolding and masking) of a monolayer colloidal crystal (MCC) template. Highly ordered, loosely packed binary and ternary surface patterns are realized by a single-step thermal treatment of a gold thin-film-coated MCC and a nonclose-packed MCC template. Our approach enables control of the parameters defining these nanoscale binary and ternary surface patterns, such as particle size, shape, and composition, as well as the interparticle spacing. This technique enables preparation of well-defined binary and ternary surface patterns to achieve customized plasmonic properties. Moreover, with their easy programmability and excellent scalability, the binary and ternary surface patterns presented here could have valuable applications in nanophotonics and biomedicine. Specific examples include biosensing via surface-enhanced Raman scattering, fabrication of plasmonic-enhanced solar cells, and water splitting

Standing Surface Acoustic Wave Based Cell Coculture

Precise reconstruction of heterotypic cell–cell interactions in vitro requires the coculture of different cell types in a highly controlled manner. In this article, we report a standing surface acoustic wave (SSAW)-based cell coculture platform. In our approach, different types of cells are patterned sequentially in the SSAW field to form an organized cell coculture. To validate our platform, we demonstrate a coculture of epithelial cancer cells and endothelial cells. Real-time monitoring of cell migration dynamics reveals increased cancer cell mobility when cancer cells are cocultured with endothelial cells. Our SSAW-based cell coculture platform has the advantages of contactless cell manipulation, high biocompatibility, high controllability, simplicity, and minimal interference of the cellular microenvironment. The SSAW technique demonstrated here can be a valuable analytical tool for various biological studies involving heterotypic cell–cell interactions

Standing Surface Acoustic Wave Based Cell Coculture

Precise reconstruction of heterotypic cell–cell interactions in vitro requires the coculture of different cell types in a highly controlled manner. In this article, we report a standing surface acoustic wave (SSAW)-based cell coculture platform. In our approach, different types of cells are patterned sequentially in the SSAW field to form an organized cell coculture. To validate our platform, we demonstrate a coculture of epithelial cancer cells and endothelial cells. Real-time monitoring of cell migration dynamics reveals increased cancer cell mobility when cancer cells are cocultured with endothelial cells. Our SSAW-based cell coculture platform has the advantages of contactless cell manipulation, high biocompatibility, high controllability, simplicity, and minimal interference of the cellular microenvironment. The SSAW technique demonstrated here can be a valuable analytical tool for various biological studies involving heterotypic cell–cell interactions

Modeling of RG13 fusion protein with a catalytically competent TEM-1 domain near the MBP fusion site to relay maltose-induced conformational changes.

<p>(A) Superpositioning of the subdomain 1 of MBP (residues 1–109 and 261–316) from maltose-free MBP (red, PDBid 1OMP), maltotriose-bound MBP (green, PDBid 3MBP), and RG13 P1 space group structure (yellow). MBP anchor/fusion points labeled ‘1′ (R316) and ‘2′ (A586(<i>319</i>)) to which TEM-1 is fused are labeled and colored as orange and red spheres, respectively. The respective MBP helices to which these two MBP anchor points are adjacent to are helices α14 and α15, respecively. The positions of S585, introduced as part of constructing RG13 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039168#pone-0039168-g001" target="_blank">Figure 1A</a>), and the TEM-1 residues 228, 229, and 230 in the RG13 fusion protein are labeled; the other connecting TEM-1 residues are shown as dashed grey lines. Shifts in the Cα positions of the α15 helix going from unbound to maltotriose bound MBP conformation are indicated by dashed arrows. (B) Close-up view of RG13 fusion site showing the MBP (yellow) and TEM-1 domains (magenta) of RG13, and the modeled position of an intact TEM-1 domain (blue, PDBid 1ERO which includes a boronic acid inhibitor to indicate the position of the active site). Modeling target points F318 (<i>230)</i> and G584 (<i>228</i>) in RG13 are shown as a grey and magenta sphere, respectively, and the equivalent positions F230 and G228 in wt TEM-1 are depicted as green spheres. The movement that is needed for G584 (<i>228</i>) in RG13 to reach the G228 position as found in wt TEM-1 is depicted by a dashed arrow. The MBP anchor point helices α14 and α15, are shown in yellow helix cartoon representation. TEM-1 β3 and β4 strands are labeled; (C) zoomed out view as in (B). TEM-1 bound boronic acid inhibitor (BAI) is shown in magenta stick representation to pinpoint the position of the TEM-1 active site. The black line and small black helix depict the RG13 residues that normally form the TEM-1 β3 and part of β4 strand yet now form the linker between the TEM-1 and MBP domains in the zinc inhibited RG13 structure. The rectangular dashed box in RG13 highlights the position of where the β3 strand used to be in an intact TEM-1 conformation.</p

Active site changes in TEM-1 domain of RG13 compared to wt TEM-1 structure.

<p>Superpositioning of wt TEM-1 structure onto the TEM domain in RG13 reveals displacement of β3 strand and part of β4 strand (inset is a zoomed in view with secondary structure elements in transparent representation). The TEM-1 β4 strand is mostly intact yet starts diverging at position R244. The α10 TEM-1 helix which is observed to be more extended in RG13. Also labeled and underlined are the MBP helices α14 and α15 that form part of the linker anchor points in the RG13 fusion protein. TEM-1 β3 strand residue positions K234, S235, A237, and β4 strand residue K244 are indicated as well as the new position of A237 with the RG13 sequence A325. The zinc ion is indicated via a grey sphere.</p

List of genes showing significantly different expression in the comparison RWT <i>vs</i>. CT.

<p>List of genes showing significantly different expression in the comparison RWT <i>vs</i>. CT.</p

The number of differentially expressed genes with opposite expression patterns annotated to KEGG pathways.

<p>The number of differentially expressed genes with opposite expression patterns annotated to KEGG pathways.</p

Zinc ion regulation in RG13.

<p>(A) RG13 (yellow and magenta) is superimposed onto wt TEM-1 (in grey). The crystallographically observed zinc binding ligands D164, H468, and E477 in RG13 are shown in ball-and-stick. Active site residues S70, E166, R244, and N276 are also shown. MBP is depicted in yellow with its anchor/fusion point helices <u>α14</u> and<u> α15</u> shown as yellow transparent rods. TEM-1 is shown in magenta with its original N- and C-terminal helices <i>α1</i> and <i>α12</i> shown in magenta transparent rods. The engineered GSGGG linker between these helices is shown in blue. The position of the original TEM-1 β3 strand position is indicated by the transparent red strand. The linkers 1 and 2 between MBP and TEM-1 are labeled 1 and 2, respectively. The positions of the RG13 residues previously shown to be involved in the zinc-mediated inhibition of RG13, H375 and H382 (i.e. TEM-1 residues 26 and 289), are shown in ball and stick and labeled. TEM-1 helix α10 is also labeled due to its close proximity to the active site, close proximity to TEM-1 α12, and observed structural differences between RG13 and TEM-1. (B) Surface representation depicting the TEM-1 fusion site and GSGGG-loop region of a modeled TEM-1 with an intact β3-β4 strand section and the GSGGG-loop within the RG13 framework. Depicted are residues H26 and H289 from the original N- and C-terminal helices of TEM-1, respectively. Also shown are residues W290 and W229 as well as the residues 230 and 228. This surface is facing the MBP domain in RG13 revealing the potential steric and structural consequences of mutations in the histidine residues.</p

Kinetic constants for nitrocefin hydrolysis and Zn²⁺ inhibition of TEM-1, RG13, and mutants thereof.

*<p>nd, not determined; however, it was confirmed that all mutants were activated by maltose like RG13 using nitrocefin assays (100 µM nitrocefin) in the presence and absence of maltose.</p